First method done: listOrganisms

egonw · Dec 20, 2015 · e976ed1 · e976ed1
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diff --git a/.gitignore b/.gitignore
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+*.Rcheck/
+*.tar.*
diff --git a/.travis.yml b/.travis.yml
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+language: r
+sudo: required
diff --git a/rWikiPathways/DESCRIPTION b/rWikiPathways/DESCRIPTION
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+Package: rWikiPathways
+Type: Package
+Title: rWikiPathways - R client library for the WikiPathways API
+Version: 0.0.1
+Date: 2015-12-20
+Author: Egon Willighagen <egon.willighagen@maastrichtuniversity.nl>
+Maintainer: Egon Willighagen <egon.willighagen@maastrichtuniversity.nl>
+Depends: jsonlite, curl, plyr
+Suggests: testthat
+Description: Use this package to interface with the WikiPathways API.
+License: MIT + file LICENSE
diff --git a/rWikiPathways/LICENSE b/rWikiPathways/LICENSE
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+YEAR: 2015
+COPYRIGHT HOLDER: Egon L Willighagen
diff --git a/rWikiPathways/NAMESPACE b/rWikiPathways/NAMESPACE
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+importFrom(jsonlite, fromJSON)
+importFrom(curl, curl, new_handle, handle_setheaders)
+importFrom(plyr, laply)
+
+export(
+  listOrganisms
+)
diff --git a/rWikiPathways/R/listOrganisms.R b/rWikiPathways/R/listOrganisms.R
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+listOrganisms <- function() {
+  handle = new_handle()
+  handle_setheaders(handle, "User-Agent" = "r/rwikipathways")
+  handle_setheaders(handle, "Accept" = "application/json")
+
+  url = paste("http://webservice.wikipathways.org/listOrganisms?format=json", sep="")
+  conn <- curl::curl(url, handle, open="r")
+  txt <- readLines(conn, warn=FALSE)
+  close(conn)
+  data = fromJSON(txt)$organisms
+}
diff --git a/rWikiPathways/man/listOrganisms.Rd b/rWikiPathways/man/listOrganisms.Rd
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+\name{listOrganisms}
+\alias{listOrganisms}
+\title{
+Lists the organisms available from the WikiPathways API server
+}
+\description{
+Lists the organisms available from the WikiPathways API server
+}
+\usage{
+listOrganisms()
+}
+\value{
+ \item{data}{the available organisms}
+}
+\examples{
+organisms <- listOrganisms()
+}
+\author{
+Egon Willighagen
+}
diff --git a/rWikiPathways/tests/testthat.R b/rWikiPathways/tests/testthat.R
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+library(testthat)
+library(rWikiPathways)
+
+test_check("rWikiPathways")
diff --git a/rWikiPathways/tests/testthat/test-listOrganisms.R b/rWikiPathways/tests/testthat/test-listOrganisms.R
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+library(rWikiPathways)
+context("Lists")
+
+test_that("organisms are found", {
+  organisms = listOrganisms()
+  expect_that(nrow(organisms), not(equals(0)))
+  expect_true("Anopheles gambiae" %in% organisms)
+})
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		YEAR: 2015
		COPYRIGHT HOLDER: Egon L Willighagen